Integrating Wikidata and other linked data sources – Federated SPARQL queries

This blog is about running federated SPARQL queries on Wikidata.  A federated query is a special type of SPARQL query that runs on more then one SPARQL endpoint. It allows access to multiple linked data resources in a single query. Below is a template of a federated query. The WikiData Query Service (WDQS) now supports federated SPARQL queries on a limited number of endpoints. Remote SPARQL...
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The Gene Wiki project: Looking to the future v.2017

The Gene Wiki project has been generously funded by the National Institutes for General Medical Sciences (NIGMS) since 2009. As the second funding period is wrapping up early next year, it was time to once again look forward and think about our vision for the next 4-5 years. Posted below is what we came up with, submitted earlier this week to the NIH as a competing renewal proposal with Lynn...
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Building communities of knowledge with Wikidata

As the Wikimedia Movement works to define its strategy for the next fifteen years, it is worthwhile to consider how its recent product Wikidata may fit into that strategy.  As its homepage states, “Wikidata is a free and open knowledge base that can be read and edited by both humans and machines.” https://www.wikidata.org/ Wikidata is a particular kind of database designed to capture...
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2016 – A busy year for Gene Wiki and WikiData

I knew it! Last year, I struggled with the year-end post for the Gene Wiki/WikiData (AKA the Gene WikiData) project because the Gene WikiData team was incredibly active. I learned my lesson, and attempted to better track their activity earlier this year with a running tally. Still, the Gene WikiData team was so productive, I still had trouble keeping up with everything they did! They’ve...
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Wikiconference North America

Wikipedia is one of the most widely used and freely accessible knowledgebases. As one of the largest, crowdsourced resources, many researchers are engaged in making the Wikimedia platform more useful in scientific research—including researchers from our lab here at The Scripps Research Institute. If you’re interested in how Wikipedia and Wikidata are being used in science, you should check out...
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Su Lab project proposal accepted to Biohackathon 2016 in Tsuruoka, Yamagata, Japan

Proposal summary: To create a model organism database web application, using Wikidata as the backend, that the microbial research community can use to load an organism and view its taxonomic information as well as genome, gene and functional annotations all in one place.  It will be simple interface with 4 frames/boxes of content (e.g. Taxonomy, Genome Browser, Gene, Gene Product), and a search...
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